v2.7.6

Author: PhilippSpahn

Scripts/CheckCharacters.py

@@ -41,8 +41,17 @@ def RunSanityCheck():
     seq = list(LibFile['seq']) 
     GeneNames0 = []
     ID0 = []    
+    
+    # --------------------------------------------------------------------
+    # Define bad characters (library)
+    # --------------------------------------------------------------------     
     BadCharacters = [' ','>','<',';',':',',','|','/','\\','(',')','[',']',\
         '$','%','*','?','{','}','=','+','@']
+        
+    # --------------------------------------------------------------------
+    # Check library
+    # --------------------------------------------------------------------         
+    BadLibCharFound = False
     for gene in GeneNames:
         for bad_char in BadCharacters:
             gene = gene.replace(bad_char,'_')
@@ -52,6 +61,7 @@ def RunSanityCheck():
             sgRNA = sgRNA.replace(bad_char,'_')       
         ID0.append(sgRNA)    
     if GeneNames != GeneNames0 or ID != ID0:
+            BadLibCharFound = True
             LibFile0 = pandas.DataFrame(data = {'gene': [gene for gene in GeneNames0],
                                      'ID': [sgRNA for sgRNA in ID0],
                                      'seq': [s for s in seq]},
@@ -67,42 +77,52 @@ def RunSanityCheck():
     Filenames = list(DataSheet['FILENAME'])
     TreatmentList = list(DataSheet['TREATMENT'])
     F = len(Filenames)
-    BadCharFound = False    
+
+    # --------------------------------------------------------------------
+    # Define bad characters (filenames & samples)
+    # --------------------------------------------------------------------         
+    BadCharacters = [' ','>','<',';',':',',','|','/','\\','(',')','[',']',\
+        '$','%','*','?','{','}','=','+','@']
 
     # --------------------------------------------------------------------
-    # Replace non-printable characters from filenames
+    # Replace non-printable characters from filenames 
     # --------------------------------------------------------------------      
     os.chdir(DataDir)    
-    BadCharacters = [' ','>','<',';',':',',','|','/','\\','(',')','[',']',\
-        '$','%','*','?','{','}','=','+','@']
+    BadFileCharFound = False        
     for j in range(F):
         Filename = Filenames[j]
         Filename0 = Filename
         for bad_char in BadCharacters:
             Filename0 = Filename0.replace(bad_char,'_')
         if Filename0 != Filename:
-            BadCharFound = True
+            BadFileCharFound = True
             os.system('mv '+"'"+Filename+"'"+' '+Filename0)
-            DataSheet['FILENAME'][j] = Filename0            
+            DataSheet['FILENAME'][j] = Filename0  
+            print("WARNING: Special characters in filenames names replaced by '_'")
 
     # --------------------------------------------------------------------
-    # Replace non-printable characters from filenames
-    # --------------------------------------------------------------------             
+    # Replace non-printable characters from sample names 
+    # --------------------------------------------------------------------   
     TreatmentList0 = TreatmentList
+    BadSampleCharFound = False 
     for bad_char in BadCharacters:
         TreatmentList0 = [str(treatment).replace(bad_char,'_') for treatment in TreatmentList0]
     if TreatmentList0 != TreatmentList:
-        BadCharFound = True
+        BadSampleCharFound = True
         DataSheet['TREATMENT'] = TreatmentList0        
+        print("WARNING: Special characters in sample names replaced by '_'")
 
     # --------------------------------------------------------------------
     # Update Data Sheet
     # --------------------------------------------------------------------            
-    if BadCharFound:
+    if BadFileCharFound or BadSampleCharFound:
         os.chdir(WorkingDir)
-        DataSheet.to_excel('DataSheet.xlsx',columns=['FILENAME','TREATMENT'])
-        print("WARNING: Special characters in sample names replaced by '_'")
-    else:
+        DataSheet.to_excel('DataSheet.xlsx',columns=['FILENAME','TREATMENT'])        
+
+    # --------------------------------------------------------------------
+    # No special characters found
+    # -------------------------------------------------------------------- 
+    if not BadLibCharFound and not BadFileCharFound and not BadSampleCharFound:
         print('No special characters found.')
 
 

Scripts/PinAPL.py

@@ -204,4 +204,7 @@
 os.system('cp configuration.yaml '+LogFileDir)
 os.system('cp PinAPL-Py.log '+LogFileDir)
 os.chdir(WorkingDir)
-os.system('cp DataSheet.xlsx '+LogFileDir)
+os.system('cp DataSheet.xlsx '+LogFileDir)
+
+# Status message
+print('LOADING RESULTS PAGE. PLEASE REFRESH PERIODICALLY...')

configuration.yaml

@@ -6,10 +6,10 @@
 # ***********************************************************************
 
 # PROJECT PARAMETERS
-ScreenType: 'depletion'               # type of screen ['enrichment'/'depletion']
+ScreenType: 'enrichment'               # type of screen ['enrichment'/'depletion']
 
 # LIBRARY PARAMETERS
-LibFilename: 'GeCKOv2_Mouse.csv'      # filename of library spreadsheet  
+LibFilename: 'GeCKOv21_Human.tsv'      # filename of library spreadsheet  
 seq_5_end: 'TCTTGTGGAAAGGACGAAACACCN'  # sequence 5' of sgRNA in read
 NonTargetPrefix: 'NonTargeting'        # prefix for non-targeting sgRNAs in library
 NumGuidesPerGene: 6                    # number of sgRNAs per gene